Overview pesticide information

Author

Stefan Kunz

Published

April 28, 2023

Cmax Pesticides

--- title: Overview pesticide information author: - name: Stefan Kunz date: last-modified format: html: self-contained: true number-sections: false number-depth: 3 anchor-sections: true code-tools: true code-fold: false code-link: false code-block-bg: "#f1f3f5" code-block-border-left: "#31BAE9" mainfont: Source Sans Pro theme: journal toc: true toc-depth: 3 toc-location: left captions: true cap-location: margin table-captions: true tbl-cap-location: margin reference-location: margin comments: hypothesis: true execute: warning: false message: false echo : false editor: visual editor_options: chunk_output_type: console --- ```{r} # ____________________________________________________________________ # Preprocessing & plotting of pesticide data for the RSQA # TODO: # - Plot chemical concentrations # - Unit of Cmax? # ____________________________________________________________________ source("/home/kunzst/Dokumente/Projects/Trait_DB/Trait-group-environment-relationships/R/Set_up.R") ``` ```{r} rsqa_cmax <- read_xlsx(file.path(path_in, "Chemicals", "RSQA Cmax only data.xlsx")) setDT(rsqa_cmax) # subset to sites where biological samples (inverts) have been taken rsqa_cmax <- rsqa_cmax[Has.Inverts.x == "y", ] # For now do not consider sediment data rsqa_cmax <- rsqa_cmax[, .SD, .SDcols = patterns("TSTAID|\\.x|\\_Cmax")] # Some of the columns containing pesticide information are characters char_tvars <- names(Filter(is.character, rsqa_cmax[, .SD, .SDcols = patterns("\\_Cmax")])) rsqa_cmax[, (char_tvars) := as.numeric(get(char_tvars))] # LF rsqa_cmax_lf <- melt(rsqa_cmax, measure.vars = patterns("\\_Cmax"), variable.name = "pesticide", value.name = "cmax") # Rm Cmax for plotting rsqa_cmax_lf[, pesticide := sub("\\_Cmax", "", pesticide)] # rsqa_cmax_lf[pesticide == "Aldicarb", max(cmax), by = "Region.x"] # Name corrections # Check which chemical names do not match with standartox # catal <- stx_catalog() # rsqa_cmax_lf[, pesticide_name_match := tolower(pesticide)] # rsqa_cmax_lf[!pesticide_name_match %in% catal$cname$variable, pesticide_name_match] %>% # unique() %>% # query_google() rsqa_cmax_lf[pesticide == "X24D", pesticide := "2,4-D"] rsqa_cmax_lf[pesticide == "Azinphosmethyl", pesticide := "Azinphos-methyl"] rsqa_cmax_lf[pesticide == "Chlorimuronethyl", pesticide := "Chlorimuron-ethyl"] rsqa_cmax_lf[pesticide == "Dacthal", pesticide := "Chlorthal-dimethyl"] rsqa_cmax_lf[pesticide == "Dimethenamid", pesticide := "Dimethenamide"] rsqa_cmax_lf[pesticide == "Kresoximmethyl", pesticide := "Kresoxim-methyl"] rsqa_cmax_lf[pesticide == "Halosulfuronmethyl", pesticide := "Halosulfuron-methyl"] rsqa_cmax_lf[pesticide == "Sulfometuronmethyl", pesticide := "Sulfometuron-methyl"] rsqa_cmax_lf[pesticide == "Parathionmethyl", pesticide := "Parathion-methyl"] rsqa_cmax_lf[pesticide == "Parathionethyl", pesticide := "Parathion"] # commonly known as parathion rsqa_cmax_lf[pesticide == "Pronamide", pesticide := "Propyzamide"] # Seems to be a formulation, active ingredient is Propyzamide rsqa_cmax_lf[pesticide == "Piperonyl.butoxide", pesticide := "Piperonyl butoxide"] rsqa_cmax_lf[pesticide == "TPM", pesticide := "Thiophanatemethyl"] #? # "propyzamide" %in% catal$cname$variable # EPTC? # catal$cname$variable[catal$cname$variable %like% "dipropylcarbamothioat"] # catal$cname$variable[catal$cname$variable %like% "eptc"] # Fentin -> which one? # Fentin acetat - fungicide # Fentin chloride - biozide, molluscicide # catal$cname$variable[catal$cname$variable %like% "fentin"] # catal$cname$variable[catal$cname$variable %like% "fentinhydroxid"] saveRDS(rsqa_cmax_lf, file = file.path(path_cache,"rsqa_cmax_lf.rds")) ``` ```{r} # Create list of plots of Cmax concentrations pl_ov_pesticides <- function(data) { ggplot(data, aes(x = TSTAID, y = cmax)) + geom_point() + coord_flip() + facet_wrap(. ~ Region.x, scales = "free") + labs(y = "Sites") + theme_bw() + theme( axis.title.x = element_text(size = 16), axis.text.x = element_text(family = "Roboto Mono", size = 12), axis.title.y = element_text(size = 16), axis.text.y = element_blank(), axis.ticks.y = element_blank(), legend.title = element_text(family = "Roboto Mono", size = 16), legend.text = element_text(family = "Roboto Mono", size = 14) ) } ls_pesticide_plots <- split(rsqa_cmax_lf, by = "pesticide") %>% lapply(., pl_ov_pesticides) ``` ### Cmax Pesticides :::: {.column-screen} ::: {.panel-tabset} ```{r} #| results: asis #| fig-width: 14 #| fig-height: 6 iwalk(ls_pesticide_plots, ~ { cat('## ', .y, '\n\n') print(.x) cat('\n\n') }) ``` ::: ::::